First, in general, a POP3 email client can usually be configured to operate in one of two ways:
1) Download and delete the server copy.
In this mode of operation, email messages are downloaded from the email server - and then the server-copy is deleted. Other email clients will not see messages after deletion. As such, a different email client, such as IMAP will subsequently see an empty mailbox after the POP3 client has deleted all downloaded content.
2) Download and leave a copy on the server
This mode of operation differs in that the POP3 client will download new messages from the email server - and leave the original email messages on the server. Other email clients will still be able to see messages in the mailbox. IMAP clients will be synchronised with the available email messages.
As to your explicit question...
If the configured email account on your iPad is configured per (1) above, then deleting the POP3 account from your iPad will delete the only existing copies of email messages downloaded from the email server. Subsequent addition of an IMAP account will not recover the messages - as they were not present on the email server.
By contrast, if the configured email account on your iPad is configured per (2) above, then deleting the POP3 account from your iPad will only delete the local copies of email messages already downloaded from the email server; all email messages still present on the email server will be untouched. Subsequent addition of an IMAP account will provide access to all messages present on the server.
I make assumption that your device configured for POP3 is configured per (2) above - but you observation other email clients that access the same mailbox - and verification of your account settings, will confirm (a) which configuration is in use and (b) the implications for future accessibility of messages on your devices.
I hope this explanation is helpful in resolving/avoiding issues.
